I am trying to run a DEG analysis for two different datasets. I want to normalize my datasets TOGETHER and then combine the expression. However, the platforms are different for the two datasets; one is a hybrid of GPL96(HG-U133A) and GPL97(HG-U133B) while the second dataset's platform is GPL10558.
please how do I combine the two datasets to be able to normalize them accordingly before running the DEG analysis?
what R codes and tools should I use for the normalization?
will doing the normalization separately affect the DEG results?